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Conserved domains on  [gi|45439357|ref|NP_057511|]
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elongin-A2 [Homo sapiens]

Protein Classification

TFIIS_I domain-containing protein( domain architecture ID 11271078)

TFIIS_I domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 544-642 2.53e-19

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


:

Pssm-ID: 462026  Cd Length: 105  Bit Score: 83.81  E-value: 2.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   544 LSDVGEVPYWVLEPVLEGWRPDQLYRRKKDNHALVRETDELRRNHCFQDFKEE------KPQENKTWREQYLRLPDAPEQ 617
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 45439357   618 RLRVMTTNIRSARGNNPNGREAKMI 642
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
8-77 5.19e-18

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


:

Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 78.89  E-value: 5.19e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45439357      8 LHAVEKLQVRLATKT-EPKKLEKYLQKLSALPMTADILAETGIRKTVKRLRKH--QHVGDFARDLAARWKKLV 77
Cdd:smart00509   1 LLRAAKKLDKVANNGkEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHknEEIRKLAKKLIKSWKKLV 73
dnaA super family cl42516
chromosomal replication initiator protein DnaA;
81-205 6.14e-06

chromosomal replication initiator protein DnaA;


The actual alignment was detected with superfamily member PRK14086:

Pssm-ID: 455861 [Multi-domain]  Cd Length: 617  Bit Score: 49.82  E-value: 6.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   81 RNTRPGPQDPEESASRQRFGEALQDQEKAWGFPENATAPRSPSHSPEHRRTarRTPPGQQRP----------HPRSHSRE 150
Cdd:PRK14086 143 RPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERD--REPYDAGRPeydqrrrdydHPRPDWDR 220

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 45439357  151 PRAERK-CPRIAPADSGRYRASPTRTAPLRMPEGPE-PAAPGKQPGRGHTHAAQGGP 205
Cdd:PRK14086 221 PRRDRTdRPEPPPGAGHVHRGGPGPPERDDAPVVPIrPSAPGPLAAQPAPAPGPGEP 277
 
Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 544-642 2.53e-19

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


Pssm-ID: 462026  Cd Length: 105  Bit Score: 83.81  E-value: 2.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   544 LSDVGEVPYWVLEPVLEGWRPDQLYRRKKDNHALVRETDELRRNHCFQDFKEE------KPQENKTWREQYLRLPDAPEQ 617
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 45439357   618 RLRVMTTNIRSARGNNPNGREAKMI 642
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
8-77 5.19e-18

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 78.89  E-value: 5.19e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45439357      8 LHAVEKLQVRLATKT-EPKKLEKYLQKLSALPMTADILAETGIRKTVKRLRKH--QHVGDFARDLAARWKKLV 77
Cdd:smart00509   1 LLRAAKKLDKVANNGkEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHknEEIRKLAKKLIKSWKKLV 73
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 7-77 1.58e-17

N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme


Pssm-ID: 238107  Cd Length: 76  Bit Score: 77.73  E-value: 1.58e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45439357   7 TLHAVEKLQVRLATKtEPKKLEKYLQKLSALPMTADILAETGIRKTVKRLRKHQ--HVGDFARDLAARWKKLV 77
Cdd:cd00183   4 VLRAKKKLEKKDSNE-EVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSneKIRKLAKALIKSWKKLV 75
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 29-77 8.40e-12

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 60.61  E-value: 8.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 45439357    29 KYLQKLSALPMTADILAETGIRKTVKRLRKH---QHVGDFARDLAARWKKLV 77
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHkenPEIKKLAKELVKKWKRLV 52
dnaA PRK14086
chromosomal replication initiator protein DnaA;
81-205 6.14e-06

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 49.82  E-value: 6.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   81 RNTRPGPQDPEESASRQRFGEALQDQEKAWGFPENATAPRSPSHSPEHRRTarRTPPGQQRP----------HPRSHSRE 150
Cdd:PRK14086 143 RPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERD--REPYDAGRPeydqrrrdydHPRPDWDR 220

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 45439357  151 PRAERK-CPRIAPADSGRYRASPTRTAPLRMPEGPE-PAAPGKQPGRGHTHAAQGGP 205
Cdd:PRK14086 221 PRRDRTdRPEPPPGAGHVHRGGPGPPERDDAPVVPIrPSAPGPLAAQPAPAPGPGEP 277
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 29-91 4.92e-04

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 42.90  E-value: 4.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45439357    29 KYLQKLSALPMTADILAETGIRKTVKRLRKH--QHVGDFARDLAARWKKLVLVDRNTRPGPQDPE 91
Cdd:TIGR01385  25 DILHQLKEFPPTEELLQETKVGVKVNKLRKHpnEDISKLAKKIIKSWKKVVDKNKSDHPGGNPED 89
DUF6264 pfam19779
Family of unknown function (DUF6264); This family of putative integral membrane proteins is ...
 136-198 2.74e-03

Family of unknown function (DUF6264); This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 179 and 218 amino acids in length.


Pssm-ID: 466182  Cd Length: 182  Bit Score: 39.56  E-value: 2.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45439357   136 PPGQQRPHPRshsREPRAERKCPRIAPADSGRYRAS-PTRTAPLRMPEGPEPAAPGKQPGRGHT 198
Cdd:pfam19779   9 PPGWQRAPIG---DPAAAAAAAPPAAPAPAAPAPPAaPAAPPAAPPPPGAPAPGAPAAARRARR 69
 
Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 544-642 2.53e-19

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


Pssm-ID: 462026  Cd Length: 105  Bit Score: 83.81  E-value: 2.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   544 LSDVGEVPYWVLEPVLEGWRPDQLYRRKKDNHALVRETDELRRNHCFQDFKEE------KPQENKTWREQYLRLPDAPEQ 617
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 45439357   618 RLRVMTTNIRSARGNNPNGREAKMI 642
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
8-77 5.19e-18

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 78.89  E-value: 5.19e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45439357      8 LHAVEKLQVRLATKT-EPKKLEKYLQKLSALPMTADILAETGIRKTVKRLRKH--QHVGDFARDLAARWKKLV 77
Cdd:smart00509   1 LLRAAKKLDKVANNGkEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHknEEIRKLAKKLIKSWKKLV 73
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 7-77 1.58e-17

N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme


Pssm-ID: 238107  Cd Length: 76  Bit Score: 77.73  E-value: 1.58e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45439357   7 TLHAVEKLQVRLATKtEPKKLEKYLQKLSALPMTADILAETGIRKTVKRLRKHQ--HVGDFARDLAARWKKLV 77
Cdd:cd00183   4 VLRAKKKLEKKDSNE-EVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSneKIRKLAKALIKSWKKLV 75
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 29-77 8.40e-12

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 60.61  E-value: 8.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 45439357    29 KYLQKLSALPMTADILAETGIRKTVKRLRKH---QHVGDFARDLAARWKKLV 77
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHkenPEIKKLAKELVKKWKRLV 52
dnaA PRK14086
chromosomal replication initiator protein DnaA;
81-205 6.14e-06

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 49.82  E-value: 6.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357   81 RNTRPGPQDPEESASRQRFGEALQDQEKAWGFPENATAPRSPSHSPEHRRTarRTPPGQQRP----------HPRSHSRE 150
Cdd:PRK14086 143 RPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERD--REPYDAGRPeydqrrrdydHPRPDWDR 220

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 45439357  151 PRAERK-CPRIAPADSGRYRASPTRTAPLRMPEGPE-PAAPGKQPGRGHTHAAQGGP 205
Cdd:PRK14086 221 PRRDRTdRPEPPPGAGHVHRGGPGPPERDDAPVVPIrPSAPGPLAAQPAPAPGPGEP 277
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 29-91 4.92e-04

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 42.90  E-value: 4.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45439357    29 KYLQKLSALPMTADILAETGIRKTVKRLRKH--QHVGDFARDLAARWKKLVLVDRNTRPGPQDPE 91
Cdd:TIGR01385  25 DILHQLKEFPPTEELLQETKVGVKVNKLRKHpnEDISKLAKKIIKSWKKVVDKNKSDHPGGNPED 89
DUF6264 pfam19779
Family of unknown function (DUF6264); This family of putative integral membrane proteins is ...
 136-198 2.74e-03

Family of unknown function (DUF6264); This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 179 and 218 amino acids in length.


Pssm-ID: 466182  Cd Length: 182  Bit Score: 39.56  E-value: 2.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45439357   136 PPGQQRPHPRshsREPRAERKCPRIAPADSGRYRAS-PTRTAPLRMPEGPEPAAPGKQPGRGHT 198
Cdd:pfam19779   9 PPGWQRAPIG---DPAAAAAAAPPAAPAPAAPAPPAaPAAPPAAPPPPGAPAPGAPAAARRARR 69
PHA03378 PHA03378
EBNA-3B; Provisional
 113-217 6.16e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 40.05  E-value: 6.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45439357  113 PENATAPRSPSHSPEHRRTARRTPPGQQRPHPRSHSREPRAERKCPRIAPADSGRYRASPTRTAPLRM-PEGPEPAAPGK 191
Cdd:PHA03378 697 PPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRArPPAAAPGAPTP 776

                         90       100
                 ....*....|....*....|....*.
gi 45439357  192 QPGRGHTHAAQGGPLLCPGCQGQPQG 217
Cdd:PHA03378 777 QPPPQAPPAPQQRPRGAPTPQPPPQA 802
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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